UGENE Genome Aligner
The UGENE Genome Aligner is a fast short-read aligner. It aligns DNA sequences of various lengths to the reference genome with a configurable mismatch rate.
It is available from the Tools ‣ NGS data analysis submenu of the main menu.
Select the Map reads to reference item to align short reads to a DNA sequence, or the Build index for reads mapping item to build an index for a DNA sequence, which can be used to optimize aligning short reads to the sequence.